Free energy simulations: Applications to the study of liquid water, hydrophobic interactions and solvent effects on conformational stability.
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Date
1985-08
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Abstract
Free energy simulations using the Metropolis Monte Carlo method and the
coupling parameter approach with umbrella sampling are described for several problems of
interest in structural biochemistry; the liquid water, the hydrophobic interaction of alkyl and
phenyl groups in water and solvent effects on the conformational stability of the alanine
dipeptide and the dimethyl phosphate anion in water. Proximity analysis of results is employed
to identify stabilizing factors. Implications of result with respect to the structural chemistry of
proteins and nucleic acids is considered.
Description
Keywords
Free energy, simulations, hydrophobic interactions, solvent effects in conformation
Citation
Beveridge D L, Mezei M, Ravishanker G, Jayaram B. Free energy simulations: Applications to the study of liquid water, hydrophobic interactions and solvent effects on conformational stability. Journal of Biosciences. 1985 Aug; 8(1&2): 167-178.